18-58968091-T-G

Variant names:

• chr18-58968091-T-G
• rs7245090
• NM_001375912.1:c.3151-10964T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375912.1(ZNF532):​c.3151-10964T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,160 control chromosomes in the GnomAD database, including 981 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.077 (981 hom., cov: 32)
• Consequence: ZNF532 NM_001375912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 1 publications found

Genes affected

ZNF532 (HGNC:30940): (zinc finger protein 532) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375912.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	NM_001375912.1	MANE Select	c.3151-10964T>G		intron	N/A	NP_001362841.1
	ZNF532	NM_001318726.2		c.3151-10964T>G		intron	N/A	NP_001305655.1
	ZNF532	NM_001318727.2		c.3151-10964T>G		intron	N/A	NP_001305656.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF532	ENST00000591808.6	TSL:1 MANE Select	c.3151-10964T>G		intron	N/A	ENSP00000468238.1
	ZNF532	ENST00000336078.8	TSL:1	c.3151-10964T>G		intron	N/A	ENSP00000338217.4
	ZNF532	ENST00000591083.5	TSL:1	c.3151-10964T>G		intron	N/A	ENSP00000468532.1

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11702 AN: 152042 Hom.: 978 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.0190

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0689

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0770 AC: 11714 AN: 152160 Hom.: 981 Cov.: 32 AF XY: 0.0750 AC XY: 5578 AN XY: 74400

African (AFR) AF: 0.211 AC: 8765 AN: 41472

American (AMR) AF: 0.0366 AC: 560 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3466

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5188

South Asian (SAS) AF: 0.0350 AC: 168 AN: 4806

European-Finnish (FIN) AF: 0.0190 AC: 202 AN: 10614

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0235 AC: 1601 AN: 68008

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0264 Hom.: 46

Bravo AF: 0.0852

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.017
DANN	Benign	0.47
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7245090; hg19: chr18-56635323;